The removal of the neonicotinoid and systemic pesticide thiamethoxam (TMX) from water and sugarcane juice by magnetic nanomodified activated carbon (AC-NP) is proposed. This adsorbent was synthesized and characterized by FTIR, XRD, and SEM, and TMX was quantified by high-performance liquid chromatography coupled to a diode array detector (HPLC–DAD). The AC-NP was efficiently synthesized using a co-precipitation method and the impregnation of magnetite (NP) in the activated carbon (AC) was assessed by the crystalline planes found in the AC-NP structure shown in the XRD diffractograms. The AC-NP FTIR analysis also indicated predominant bands of Fe–O stretching of the magnetite at 610–570 cm−1. Functional groups in AC and AC-NP were identified by absorption bands at 3550 and 1603 cm−1, characteristic of O–H and C = C, respectively. The TMX adsorption kinetics in sugarcane juice was the pseudo-second-order type with r2 = 0.9999, indicating a chemical adsorption process. The experimental sorption capacity (SCexp) for both TMX (standard) and TMX-I (insecticide) by AC-NP were 13.44 and 42.44 mg/g, respectively. Seven non-linear isotherm models (Langmuir, Freundlich, Dubinin-Radushkevich, Toth, Hill, Sips, and Redlich-Peterson) were fitted to the experimental adsorption data of TMX and TMX-I by AC-NP. Considering the standard error (SE), Freundlich, Langmuir, and Sips were the most appropriate models to describe the TMX adsorption, and Hill’s best adjusted to TMX-I experimental data. The chromatographic method was highly satisfactory due to its high selectivity and recovery (91–103%). The efficiency of AC-NP in the sorption of TMX was confirmed by the excellent values of SCexp and sorption kinetics.